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After the X-files were closed in 1994, Scully and her FBI partner, Fox Mulder, were reassigned to other sections and Mulder was partnered with AgentAlex Krycek. (TXF: "The Erlenmeyer Flask", "Sleepless") However, Krycek was secretly working for the Cigarette Smoking Man, and in a Syndicate meeting primarily involving Krycek and his superior shortly after he had investigated his first case with Mulder, Krycek reported that Scully was a much larger problem than the CSM had described. The CSM mysteriously replied that "every problem has a solution" and sinisterly stubbed out a cigarette he had been smoking. (TXF: "Sleepless")

Soon thereafter, Mulder became involved in a hostage situation in which he was taken captive by Duane Barry, a crazed self-professed alienabductee who was insistent on not being taken again and hoped that – by taking someone else to the site from where he had first been abducted – he might save himself from such an outcome, as he believed that his companion would be abducted instead of him. Barry had difficulty with remembering where that site was, but believed that a group would tell him the location's whereabouts. The person who Barry originally intended to take with him was his original hostage, DoctorDel Hakkie, but due to Mulder intentionally giving Barry some misleading advice, Barry was shot, freeing Mulder and Dr. Hakkie from his captivity. However, Barry subsequently managed to escape from a hospital where he had been taken. (TXF: "Duane Barry")

At one point prior to Scully's kidnapping, her mother, Margaret, had a dream about her being taken away. Mrs. Scully intended to call Dana with news of the dream but feared that, by doing so, she might only scare her daughter. (TXF: "Ascension")

Shortly after his escape, Duane Barry kidnapped Scully from her home, bursting through her window while she was recording a phone message for Mulder about a metallic implant that had been recently removed from Duane Barry's body. (TXF: "Duane Barry", "Ascension")

A scene of "Ascension" implies that Krycek provided Duane Barry with Scully's address.

Scully's message to Mulder alerted him to her situation (when he listened to the recording later that night) and he rushed to the crime scene, where he met with Margaret Scully, who was shocked to find that her daughter was missing and told Mulder about the dream she had experienced.

Scully had been gagged, bound and forced into the trunk of Barry's car by 11:23 the next morning, at which time Barry was driving along Route 229 in Rixeyville, Virginia with her in the vehicle's boot. Moments later, the vehicle was pulled over by a Patrolman who grew suspicious of Barry. The Patrolman heard Scully cause a commotion inside the boot and this distraction allowed Barry an opportunity to shoot the other man. Barry took the opportunity and opened the boot to look at Scully, unaware that a camera inside the Patrolman's car – parked just behind Barry's vehicle – was meanwhile recording the scene.

At 3:11 p.m., Mulder – who had not slept and had been ordered to go home – nevertheless analyzed footage from the Patrolman's camera at the Video Production Unit of FBI Headquarters; the footage established for the FBI that Scully was still alive. Mulder then determined, while in the company of Agent Krycek, that Barry intended to take Scully to Skyland Mountain and Mulder decided to head after her. Krycek secretly called the CSM with this news, vowing to hold Mulder off until Scully was located by a group that Krycek did not name. Mulder did not inform his FBI superior, Assistant DirectorWalter Skinner, that he knew where Barry was going, as Mulder feared that – if Skinner sent an FBI task force after Barry – the crazed, alleged abductee might do something even more manic.

Meanwhile, Barry and Scully arrived near the base of Skyland Mountain where Barry spoke to a Tram Operator who did not notice Scully but instructed Barry to take a side road to the mountain's summit, a journey that would take a little more than an hour. A little more than forty-five minutes after this encounter, Mulder dangerously raced toward the top of the mountain in the tram while its operator and Krycek remained at the bottom of the incline but, when Mulder was almost at the summit, his progress was delayed by Krycek, who killed the tram operator and stopped the tram before calling his superior to report that he was stalling Mulder until advised to do otherwise. Barry reached the summit just as Mulder began to realize that he might have to climb the rest of the way. As he clambered onto the tram's roof, however, Krycek restarted the tram.

By the time Mulder finally arrived at the summit, Barry had abandoned his car, with its radio left on, and had taken Scully out of the trunk, leaving her necklace inside it. Mulder found this deserted scene, upon his arrival, and was witness to an immensely bright light beaming from an airborne craft that sped away. Apparently, Scully had been abducted from the mountain top. (TXF: "Ascension")

Moments after the bright light in the sky rushed away, an ecstatic Duane Barry exclaimed to Mulder that Scully had been taken by a group that Barry did not name but implied that they were the same group whom he had referred to, upon warning Mulder that they would take someone else. When he saw another bright light in the sky, Barry fearfully thought that the group had returned for him, but the light was merely from a Search and Rescue helicopter and the two men were transported to safety by 8:46 p.m.. Five teams were dispatched to search the mountain for the missing FBI agent.

Undergoing questioning by Mulder, Barry repeated his claim that Scully – rather than him – had been taken by a group, swearing that he had not killed her. He also alleged that he had obtained injuries from the craft that had sped away, which he referred to as a "ship" even though Mulder maintained that the first bright light he had seen in the sky had been a helicopter. Barry insisted that the military knew where Scully was. Mulder was initially highly suspicious that Barry himself had hurt Scully, despite Barry denying such a possibility. An apologetic Duane Barry told Mulder that the group had to take her and that he hoped they were not hurting her too much with their tests.

Krycek thereafter encountered considerable trouble with learning what had happened to Scully. After noticing that he had been talking with Barry, Mulder privately queried Krycek on whether he had asked Barry about Scully; Krycek confirmed that he had, adding that Barry had responded by whistling "Stairway to Heaven", but Barry died soon thereafter. When asked by Krycek about Scully, the CSM revealed that his group had taken care of that issue but refused to divulge any further information to Krycek.

In a hearing with AD Skinner and members of the FBI's Office of Professional Responsibility, Mulder recounted that he had questioned Barry about Scully. He also claimed that the military knew where Scully was but were, because of this, covering up the actual cause of Barry's death, but this line of thinking was thought to be "paranoid" by one of the FBI members at the meeting.

When Mulder went to see SenatorRichard Matheson to find out if he could help, Mulder was confronted by his informer, X, who told Mulder that Senator Matheson could not lend his assistance. Mulder suspected X of knowing what had happened to Scully, demanding that X confirm or deny whether he did, but X was typically unforthcoming with any clear answers.

Nonetheless, Mulder then discovered Krycek's involvement with the CSM and began to suspect his involvement in Scully's abduction. While meeting alone with Skinner to report his own suspicions regarding Krycek, Mulder testified that, when he had reached the top of Skyland Mountain, he had seen an unmarked helicopter working in the area and that he now believed Krycek had given away the whereabouts of Scully and Barry to an agency that Krycek was working with and the CSM was working for. Mulder argued that the reason Scully had been abducted was either because she had gotten too close to whatever it was the agency was trying to deny, had obtained hard and damning evidence – the metallic implant in her possession – or because her termination would prevent further involvement with Mulder and his work. Influenced by Mulder making such a statement, Skinner wondered if he thought Scully was dead, but Mulder admitted to being unsure as to whether she was.

When Mulder subsequently met with Mrs. Scully, she was immediately curious to know if he had any news that her daughter was all right. Despite Mulder admitting that the FBI had no further information about Agent Scully, Mrs. Scully remarked that she knew Mulder was doing all he could. Mrs. Scully confessed that she had experienced the same dream about Dana being taken away and commented that she was extremely scared by the dream but Mulder thought it would be scarier for someone in Mrs. Scully's position if they stopped having the recurring dream. He showed her the necklace he had found and they both commented on the item; even though Mulder intended to deliver it to Mrs. Scully, she told Mulder to give it to Agent Scully when he found her. Mulder agreed and returned to Skyland Mountain in lonesome remembrance of his missing FBI partner. (TXF: "Ascension")

Shortly after Skinner reopened the X-files, Mulder carried a folder containing Scully's belongings upon his return to his X-files office. (TXF: "Ascension", "3") From the folder, he put a relatively new X-file pertaining to Scully (labeled 73317) into storage, inside a file cabinet in the room, as well as her badge and glasses, removing Scully's cross from inside her badge before placing her other belongings into the cabinet.

Mulder then started to investigate a trio of vampires known as the Trinity Killers but, soon after he began investigating them, a CommanderCarver remarked with surprise that Mulder was an FBI agent without a partner and seemed to want to work that way.

When Kristen Kilar (an associate of the Trinity Killers) first met Mulder – in Club Tepes – she realized that Mulder had lost someone and that the person had been a friend, not a lover. She later noticed that he was wearing Scully's cross and, though Kristen Kilar half-jokingly guessed that he was doing so because he was trying to ward her off, he explained that the cross was from someone he had lost. She hoped he found the person, correctly assuming both that the person could be found and that the person was a female. Kirsten Kilar killed herself soon thereafter and, moments after learning of her death, Mulder withdrew Scully's necklace from under his shirt to momentarily look at it. (TXF: "3")

Not long thereafter, Mrs. Scully told Mulder a story of how, one day when Dana Scully had been a young girl, she had made an effort to join in with her brothers by shooting at a snake but had later realized what she had done and unsuccessfully tried to keep the snake alive. By this time, Mrs. Scully had had a headstone for her daughter, Dana, crafted, despite Mulder believing that it was too soon to give up. He had brought paperwork about Scully's abduction home with him, including an image of a gagged Dana Scully and the X-file on her that he had opened. (TXF: "One Breath")

While she was gone, Scully was experimented on, in a white-lit place. (TXF: "Ascension", "One Breath", et al.) The individuals who performed the tests were men, one of whom was Dr. Shiro Zama. (TXF: "Nisei", "731") A group of female members from the Mutual UFO Network saw Scully during her abduction. Although most of these other women were repeaters, the men never revealed themselves to the women, instead removing the females' memories of their abductions even though those memories somehow repeatedly started to seep back. (TXF: "Nisei")

A tiny computer chip was implanted subcutaneous to the back of Scully's neck, during her own abduction, which Scully was told had the capability to read her thoughts. (TXF: "The Blessing Way", "Nisei", et al.) This chip was manufactured by a Japanese company and had been mailed to Dr. Zama in Perkey, West Virginia. (TXF: "731")

At one point during her abduction, a dazed Scully opened her eyes to see three doctors standing over her, wearing white surgical gowns and masks with goggles. An unmasked Dr. Ishimaru leaned down near her and she tilted her head to look up at him blankly as he began to tie a small mask over his face. (TXF: "Nisei")

This scene, shown in flashback, was presumably when the doctors were about to implant the chip into Scully's neck.

One another occasion, Scully lay on an operating table in a white-lit room where crosses of light shone over her arms and two figures watched from nearby. A spinning drill approached her from above and Scully's eyes suddenly opened. A suction-like tube, seemingly attached to her belly button, began to inflate her stomach, which grew very large as the procedure continued to be observed by the nearby figures. (TXF: "Ascension")

Branched DNA was added to Scully's blood during her abduction. This highly sophisticated form of DNA had the possible applications of being a tracking system, the developmental stages of a biological marker or part of an effort to graft a human to something inhuman. (TXF: "One Breath")

Shortly after her mother had told Mulder the story of her early encounter with a garter snake, Scully was returned and taken to the Intensive Care Unit of Northeast Georgetown Medical Center. She was comatose and hooked up to various machines when NurseWilkins arrived for the evening shift. Scully was in critical condition with complete unawareness of self or environment, exhibiting no evidence of language comprehension or of voluntary responses to external stimuli. Her immune system had been decimated and her blood contained abnormal protein chains, with a highly unusual amino acid sequence. The protein chains were by-products of the branched DNA that was now an inactive waste product and constituted a biological poison.

On the same night when Nurse Wilkins found Scully in this condition upon arriving for the evening shift, Mulder received a call that informed him of Scully's return. He hurried to see her (bursting into her ward, even though it was off-limits to anyone but authorized personnel) but Mrs. Scully had made her way there before him and was visiting her daughter upon his arrival. Doubting that Agent Scully had simply just arrived, an angry Mulder considered the possibility that she had been brought to the hospital by paramedics, FBI or military and that, whoever they had been, a Dr. Daly might be working with them. Daly later apologetically notified both Mulder and Mrs. Scully, however, that no-one at the hospital could determine how Agent Scully had arrived there, been administered, or how she had been attended to in such a critical condition.

Because Scully had been away for so long, there was an absence of her recent medical history, so Daly was unsure how long she had been in such a state and was therefore at a loss for a prognosis. By the time the doctor delivered this news to Mulder and Mrs. Scully, the facility's staff had conducted every possible test on Agent Scully, determining that there were no indications of acute injuries – traumatic or non-traumatic – and finding no signs of degenerative or metabolic disorders; the medical staff consequently did not know why Scully was in such a condition. Despite Mulder requesting that she be examined for trace evidence, Scully had been bathed and cleaned since her admittance. As Daly had been informed by the FBI, Scully had a living will that Mulder had signed as a witness and the will indicated that Scully did not wish to live in such a critical condition.

Her sister, Melissa, believed she could sense Dana's soul, including her thoughts, and tried to show Mulder her own method of doing so. In fact, Dana Scully saw both her sister and Mulder in a reality she was conscious of, wherein her visitors stood on a dock as she watched them from a small boat, tied to the dock but far from it. Mulder found the method to be unsuccessful, concluding it was nothing more than waving his hands in the air, but Melissa claimed that was because his fear and anger were blocking any positive emotions Dana needed to feel.

The comatose Agent Scully was thereafter visited by Melvin Frohike, who noticed an anomaly in her medical charts and smuggled them out of the hospital. After Mulder and Frohike took the charts to the other Lone Gunmen, they learned of the branched DNA, with the remote help of a hacker known as "the Thinker". This evidence established, for Mulder and the Gunmen, that whoever had been experimenting on Scully had no intention of continuing to do so. When asked by Mulder if Scully would survive, Byers – aware of the decimation of Scully's immune system – doubted that even a healthy human body had the ability to combat the biological poison that was now in her blood.

Blood was subsequently taken from Scully's ravaged body by Nurse Wilkins but was stolen by a man who Mulder chased until once again being confronted by X, who insisted that he accept Scully's death and stop searching for whoever had experimented on her. The man who had taken Scully's blood would not reveal who wanted it, when Mulder finally captured him, and was killed by X, moments later.

Dr. Daly, Mrs. Scully, Mulder and Melissa Scully then gathered to discuss the fate of Agent Scully, who was now below the criteria established in her will. Dr. Daly believed that Dana Scully was in such a critical condition that she could not survive if she was disconnected from her respirator, as he suspected that she had been in her current state ever since her disappearance and that she would not improve. Mulder was insistent that his former partner be experimented on with designer antibiotics, which he claimed was a possible treatment for branched DNA, but this suggestion was opposed by both Dr. Daly – who considered Mulder's diagnosis of Scully's condition as being too unconventional – and Melissa Scully – who wanted her sister to be treated in as natural a way as possible. Mrs. Scully, the deciding vote of the collective, acknowledged that her daughter had already made the decision and regretfully explained that she herself was choosing to respect that decision. Even though Mrs. Scully invited Mulder to join the Scully family in ceasing Dana's mechanical ventilation, Mulder declined the offer.

In the pier-like comatose realm that Agent Scully was aware of, she watched in silence as the rope that tied her boat to the distant dock broke, causing her small vessel to drift from the shore.

During a follow-up meeting with Skinner regarding the robbery of Scully's blood, Mulder implied accusations that the Cigarette Smoking Man had been responsible for not only what had happened to Scully but also the stealing of her blood. Implying that he didn't believe Scully would survive, Skinner told Mulder, "Agent Scully was a fine officer. More than that, I liked her. I respected her." Mulder wondered about the implications if he himself had known the potential consequences of working for the FBI but had never told her, to which Skinner replied that he was therefore as much to blame for Scully's condition as the CSM was.

Scully meanwhile experienced a reality in which she was lying on a table, wearing a white gown with her eyes closed, in a void-like area as her deceased father, dressed in military attire, apparently visited her. He poetically mused over his life and told her of his distress at learning that he would never see her again, ultimately telling her that – although they would be together again – that time had not yet come.

Meanwhile, Melissa Scully assured a depressed Mulder that, even if he spent the rest of his life finding everyone who was responsible for Scully's condition, it still wouldn't bring her back but that those people had a horror equal to Scully's condition coming to them. Much to Melissa's confusion, Mulder suggested that the people responsible for Scully's condition included himself.

Mulder thereafter gained access to the CSM's home and threateningly demanded to know the answers to several questions, starting with why Scully had been taken rather than himself, but the CSM hesitated before answering. Although he evaded Mulder's question, the CSM implied that the reason Scully had been returned was because he liked both her and Mulder.

Soon after, Agent Mulder again encountered X who, this time, admitted that he was unwilling to reveal why Scully had been taken because the issue was too close to himself. X nevertheless told Mulder that a group of armed men – who X implicated as being the same men who had taken Scully – would be coming to his apartment that night, to search for information they believed Mulder had about her.

That night, Mulder was consequently waiting in his apartment for their arrival when Melissa Scully arrived, delivering news to him that Agent Scully was – according to Dr. Daly – weakening and that her death could therefore be at any time. Even though Melissa Scully expected Mulder to want to visit Agent Scully, he explained that he couldn't, at that time. Melissa Scully criticized Mulder's depression, telling him it would not help Agent Scully. Even though Mulder – following Melissa's departure – initially returned to waiting for the armed men to arrive, he visited Agent Scully shortly after and told her that, although he felt that she strongly believed she was not ready to pass away and he was unsure whether his presence would help bring her back, he would nevertheless stay with her. Mulder remained at Scully's bedside, as per his word, but returned to his apartment on the following morning, finding that his home had been wrecked while he had been with Scully.

She, seeing herself surrounded by an autumn woodland scene, eventually became more aware of her actual surroundings, regaining consciousness. Nurse Wilkins was the first to see that she was coming to, her eyes fluttering slowly open, so the nurse requested that Dr. Daly be called immediately. Shortly after, Mulder was pleased to receive news of Scully's revival, via telephone. By the time he returned to the hospital to visit her, Scully had been moved into a room of her own, where her mother and sister were also present during Mulder's visit. Despite his first concern being how she was now feeling, she let him know that she could not remember anything after an unspecified event involving Duane Barry, but he assured her that her lack of memory didn't matter. Upon him handing her a gift he had brought with him – a video of Superstars of the Super Bowl – Scully joked that she had known there had been a reason to live. She also let him know that she had had the strength of his beliefs and he returned her necklace to her. Scully was later in her new room when she learned, from Nurse Wilkins, that Nurse Owens – who Scully was convinced had watched over her in the Intensive Care Unit – had actually never worked at the hospital. (TXF: "One Breath")

On their first case together since before Scully's abduction, Mulder twice intermittently became concerned about her involvement, at least initially thinking she should possibly take some time off. However, Scully was very eager to work, insisted that she had already lost enough time and perceived a need for both of them to get past the issue regarding her participation, as she was back to stay. (TXF: "Firewalker")

In 1995, after a computer chip was removed from the base of Scully's neck but she realized that she had no memory of it being put there, her sister referred her to Dr. Mark Pomerantz, who induced a form of hypnosis in which Scully apparently recalled several details about her abduction experience. She stated that the incident had involved time loss and that, just before she had been taken away, she had feared she would die. Scully spoke of men, saying that one of them had taken her. She also seemingly recalled that there had been a light, loud sounds that caused her ears to pound and an alarm. According to her, the others present during her abduction had wanted to know if she was alright and she had felt a need to trust someone, as she had been powerless and could not resist them. Scully abruptly came to her senses upon Dr. Pomerantz lightly touching her hands, after which she concluded that the hypnosis didn't seem to be working and hurried away. (TXF: "The Blessing Way")

Shortly thereafter, she and Mulder found a massive mountain vault that included many medical files, one of which pertained to Scully herself and contained a tissue sample that was - unlike in the other files - recent. The next morning, Mulder told Skinner that one of the things he wanted to find out - by keeping a digital tape copy of the MJ documents, rather than handing it over to the conspirators in return for the agents' protection - was the exact nature of whatever it was that the conspirators had done to Scully. Not long after this, Mulder insisted to Scully that the files inside the mountain vault had been cataloging abductees. (TXF: "Paper Clip")

Later that year, an investigation into the murder of MUFON member Steven Zinnzser brought Scully to find the group of female MUFON members, including Lottie Holloway and Penny Northern, who had seen her in the white-lit place. While she talked to them at length, she privately recalled brief flashes from her abduction. The women seemed to recognize Scully almost immediately and explained where they knew her from but she could not remember ever having seen them before and admitted to being unready to discuss their shared experience, a fear to remember which all the other women could relate to. The women expected that Scully's memories of her disappearance may have started to come back to her but without making sense and knew that the first memories to return were the light and then, occasionally, the faces of the male experimenters. Like Scully, each woman had had an implanted computer chip removed from the back of their own neck. Collectively, they told Scully they were all dying from a cancerous ailment due to their abduction experiences. Scully privately found their information to be "freaky." (TXF: "Nisei")

However, she continued to make more discoveries related to her abduction; the case involved Dr. Zama, whom she recognized, and she also had her implant analyzed, learning of the extraordinary computing power of such technology. (TXF: "Nisei", "731") She soon after came to the belief that the place where her abductors had taken her and put the implant in her neck was one of several train cars operating on an elaborate secret railroad. (TXF: "731")

While Scully was suffering from a paranoid psychosis on the night of 1 May 1995, she made several accusations to Mulder directly, claiming that he was one of the people who had abducted her and that he had put the implant in her neck. However, Scully began to recover soon thereafter and had been hospitalized by the afternoon of the next day. (TXF: "Wetwired")

After Scully became romantically involved with the psychotic Ed Jerse – who was under the influence of an unusual tattoo – but managed to escape from him, Mulder congratulated her on becoming the first person ever to make personal appearances in the X-files on two separate occasions, indirectly referring to her earlier presence in the X-file concerning her abduction. (TXF: "Never Again")

The storyline of Scully's abduction was created to cover the forthcoming absence of actress Gillian Anderson, who had unexpectedly discovered – halfway through the first season of The X-Files – that she was pregnant with her first child. Frank Spotnitz later stated, "The mythology of the series didn't really blossom until [then] [....] [The pregnancy] forced The X-Files to be serialized in a way I don't think it was ever intended to be serialized. Suddenly, there had to be an arc of stories that dealt with the fact that Scully was going to be gone for who-knew-how-many episodes." ("Threads of the Mythology: Abduction", The X-Files Mythology, Volume 1 - Abduction special features) According to Spotnitz, "The 'mythology', quote-unquote, was very undefined at that point. There had been some mythology episodes the first year of the series, but I don't think anybody really looked at it as mythology, if you will, at that point." Spotnitz also characterized Anderson's pregnancy as the catalyst that "really began the mythology in earnest, or kicked it into a higher gear anyway." ("The Truth About Season 2", TXF Season 2 DVD special features) Noted writer Howard Gordon, "Fortunately, this is a show about abduction, so we abducted her." ("Threads of the Mythology: Abduction", The X-Files Mythology, Volume 1 - Abduction special features) Regarding the lingering effects Anderson's pregnancy had, Gordon elaborated, "Ultimately it sort of was a blessing in disguise because it forced us to contrive something that has been grist for the mill and will continue to be, in terms of her abduction or disappearance. As it turned out, her pregnancy not only gave birth to [Anderson's daughter] Piper, but to a whole new avenue of possibilities on the show." (X-Files Confidential, p. 87) Spotnitz confirmed the show's writers tried to account for the actress' absence by devising the idea Scully would be abducted specifically "by aliens." ("The Truth About Season 2", TXF Season 2 DVD special features) As David Duchovny pointed out, Scully's abduction had similarities to the abduction of Mulder's sister, Samantha, which helped provide the relationship between the two FBI agents with even more emotional resonance. (The Truth Is Out There: The Official Guide to The X-Files, p. 25)

The decision to have Scully be seen bound and gagged in the boot of Duane Barry's car, in the episode "Ascension", proved controversial. Chris Carter reflected, "I remember that the censors were very nervous about us putting Scully in a trunk and also we were very nervous about putting a pregnant Scully in a trunk, but she was just a champ, she got in that car and you walk this fine line on television trying not to be too graphic and that was one of those images that we fought for and it made the show very scary because you believe that Agent Scully was really in danger in the hands of a psycho and that she was riding around in that back of car as it was climbing that mountain." ("Chris Carter Talks About Season 2 Episodes: Ascension", TXF Season 2 DVD special features)

A shot of Scully with an enlarged stomach, in "Ascension", actually features Gillian Anderson's pregnant torso; the producers realized they could take advantage of the pregnancy by making Anderson's enlarged belly seem the result of peculiar experiments. (The Complete X-Files: Behind the Series, the Myths and the Movies, p. 57) The actress left routinely working on the series about a week before her child – Piper Maru Anderson, a daughter – was born and the actress belatedly gave birth a few weeks after she had appeared in the aforementioned scene of "Ascension", on 25 September 1994. Her daughter was delivered via cesarean section, which was unanticipated and required that Gillian Anderson spend the next six days in hospital. Meanwhile, her absence from the set of The X-Files facilitated the filming of "3", the first ever episode in the series in which Scully does not appear. Four days after Gillian Anderson's period of hospitalization, she was back working on The X-Files, filming scenes for the episode "One Breath".

Frank Spotnitz summed up the effect Gillian Anderson's pregnancy ultimately had on the series, "It was sort of a happy accident and there is a beautiful irony in all that because, ultimately, Gillian Anderson's real-life pregnancy leads to the storyline about Scully not being able to have a baby and then miraculously, by the end of the series, having a child and all of that is a piece, and it's a wonderful sort of blur of real life and fiction, because it was all, you know, one would not have happened without the other. If Gillian Anderson had not had Piper in Season 1 of The X-Files, the show never would have evolved the way it did." ("Threads of the Mythology: Abduction", The X-Files Mythology, Volume 1 - Abduction special features)

Although "Ascension" and "Memento Mori" use original footage to show the white-lit location where Scully is tested upon, archive footage from "Ascension" is used in both "Nisei" (together with original footage of the setting) and "The Truth" (using footage exclusively from "Ascension"). "Nisei" first features an original shot of Scully's face, with her eyes closed, before later showing a shot from "Ascension" of a drill descending toward Scully. Another shot in a subsequent scene of "Nisei" is the same shot from "Ascension" that features Gillian Anderson's pregnant torso. A later scene of "Nisei" features the original shot of Scully from earlier, amid footage of surgically masked scientists peering down at Scully as she druggily opens her eyes to them. A segment of archive footage that accompanies Scully's testimony in "The Truth" includes a shot of the bright light in the sky speeding away, a sped-up shot that pans down from Scully's captors to her herself, a shot of Scully opening her eyes and the start of a close-up shot of Scully's torso being enlarged.